The replication of murine leukemia virus (MuLV) requires the capture of a cellular tRNA(Pro) as a primer for reverse transcription. To further study the specificity of primer selection, we have utilized a defective MuLV in which the primer-binding site (PBS) has been altered to be complementary to a nonmammalian tRNA, yeast tRNA(Phe). Infectivity of the defective MuLV is dependent upon co-expression of yeast tRNA(Phe) in the cell. Defective MuLV genomes have been constructed in which the PBS was altered to be complementary to tRNA(Phe) that also encoded the cDNA for tRNA(Phe). Transfection of these defective proviral genomes into cells resulted in the production of infectious MuLV as determined by a single-round assay. The amount of infectious virus produced using this complementation system, though, was approximately 6-fold lower than that produced following transfection of defective proviral genomes with a wild-type PBS complementary to tRNA(Pro). The lower infectivity was not due to reduced expression of tRNA(Phe) in the transfected cells as compared to endogenous tRNA(Pro) or tRNA(Lys,3). Serial passage of the MuLV genome with a PBS complementary to tRNA(Phe) that encoded tRNA(Phe) resulted in amplification of the virus. Using this rescue system, we have passaged the virus for four serial passages, after which time a revertant genome in which the PBS was altered to be complementary to tRNA(Gln) was detected that grew to high titers following subsequent serial passage. The results of these studies suggest that MuLV has preferences for the tRNA primer used in reverse transcription and are discussed with respect to the mechanism of primer selection.
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http://dx.doi.org/10.1016/j.virol.2004.03.013 | DOI Listing |
RNA
November 2024
Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
Uridine residues present at the wobble position of eukaryotic cytosolic tRNAs often carry a 5-carbamoylmethyl (ncm), 5-methoxycarbonylmethyl (mcm), or 5-methoxycarbonylhydroxymethyl (mchm) side-chain. The presence of these side-chains allows proper pairing with cognate codons, and they are particularly important in tRNA species where the U residue is also modified with a 2-thio (s) group. The first step in the synthesis of the ncm, mcm, and mchm side-chains is dependent on the six-subunit Elongator complex, whereas the thiolation of the 2-position is catalyzed by the Ncs6/Ncs2 complex.
View Article and Find Full Text PDFBiochemistry
August 2024
Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States.
Yeast phenylalanine tRNA (tRNA) is a paradigmatic model in structural biology. In this work, we combine molecular dynamics simulations and spectroscopy modeling to establish a direct link between its structure, conformational dynamics, and infrared (IR) spectra. Employing recently developed vibrational frequency maps and coupling models, we apply a mixed quantum/classical treatment of the line shape theory to simulate the IR spectra of tRNA in the 1600-1800 cm region across its folded and unfolded conformations and under varying concentrations of Mg ions.
View Article and Find Full Text PDFJ Biol Chem
August 2024
Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan. Electronic address:
Archaeosine (G) is an archaea-specific tRNA modification synthesized via multiple steps. In the first step, archaeosine tRNA guanine transglucosylase (ArcTGT) exchanges the G15 base in tRNA with 7-cyano-7-deazaguanine (preQ). In Euryarchaea, preQ15 in tRNA is further modified by archaeosine synthase (ArcS).
View Article and Find Full Text PDFACS Omega
June 2024
Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America.
All organisms methylate their nucleic acids, and this methylation is critical for proper gene expression at both the transcriptional and translational levels. For proper translation in eukaryotes, 2'--methylation of C (Cm) and G (Gm) in the anticodon loop of tRNA is critical, with defects in these modifications associated with human disease. In yeast, Cm is formed by an enzyme that consists of the methyltransferase Trm7 in complex with the auxiliary protein Trm732, and Gm is formed by an enzyme that consists of Trm7 in complex with Trm734.
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
March 2024
University of Connecticut, Storrs, Connecticut 06269, United States.
Established bottom-up approaches for the characterization of nucleic acids (NAs) rely on the strand-cleavage activity of nucleotide-specific endonucleases to generate smaller oligonucleotides amenable to gas-phase sequencing. The complexity of these hydrolytic mixtures calls for the utilization of a front-end separation to facilitate full mass spectrometric (MS) characterization. This report explored the merits of microfluidic capillary zone electrophoresis (CZE) as a possible alternative to common liquid chromatography techniques.
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